1887

Abstract

Two reddish-coloured bacterial strains (HMF7604 and HMF7620) were isolated from bark of birch tree () together with two strains (designed as HMF7603 and HMF7618). Cells were observed to be Gram-stain-negative, oval- to short rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four isolates belonged to the genus , family . They had the highest similarities (95.4–95.6 %) to ID1504, with which they formed a clade in phylogenetic trees. Menaquinone-8 was the only respiratory quinone. The predominant fatty acids were summed feature 3 (C 7 and/or C 6), C 6, C and C. Strain HMF7604 contained two unidentified phosphoglycolipids, nine unidentified glycolipids, one unidentified aminolipid, three unidentified phospholipids and three unidentified polar lipids, while strain HMF7620 contained one unidentified phosphoglycolipid, four unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified polar lipid. The DNA G+C contents of strains HMF7604 and HMF7620 were 65.6 and 65.7 mol%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between the two isolates and their close relative were 81.1–95.3 and 24.5–61.6 %, respectively. Based on the results of phenotypic and phylogenetic characterizations, the four isolates are considered to represent two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are HMF7604 (=KCTC 43354=NBRC 115489) and HMF7620 (=KCTC 43051=NBRC 113959).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005531
2022-10-17
2024-05-18
Loading full text...

Full text loading...

References

  1. Brooks BW, Murray RGE. Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Evol Microbiol 1981; 31:353–360 [View Article]
    [Google Scholar]
  2. Rainey FA, Nobre MF, Schumann P, Stackebrandt E, da Costa MS. Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 1997; 47:510–514 [View Article] [PubMed]
    [Google Scholar]
  3. Battista JR, Rainey FA. Deinococcus. In Bergey’s Manual of Systematics of Archaea and Bacteria New Jersey: Wiley; 2015 pp 1–13
    [Google Scholar]
  4. Ten LN, Cho H, Cho YJ, Jung HY. Deinococcus terrigena sp. nov., a novel member of the family Deinococcaceae. Antonie van Leeuwenhoek 2019; 112:389–399 [View Article] [PubMed]
    [Google Scholar]
  5. Kim D-U, Jang JH, Kang M-S, Kim J-Y, Zhang J et al. Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil. Int J Syst Evol Microbiol 2018; 68:3232–3236 [View Article] [PubMed]
    [Google Scholar]
  6. Makk J, Enyedi NT, Tóth E, Anda D, Szabó A et al. Deinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary. Int J Syst Evol Microbiol 2019; 69:1724–1730 [View Article] [PubMed]
    [Google Scholar]
  7. Wang X-P, Li C-M, Yu Y, Li H-R, Du Z-J et al. Deinococcus arcticus sp. nov., isolated from Silene acaulis rhizosphere soil of the Arctic tundra. Int J Syst Evol Microbiol 2019; 69:3437–3442 [View Article]
    [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 125–175
    [Google Scholar]
  9. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  11. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  17. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article]
    [Google Scholar]
  18. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  20. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  21. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  23. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  25. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  26. Doetsch R. Determinative methods of light microscopy. In Gerhardt P. eds Manual of Methods for General Bacteriology American Society for Microbiology; 1981
    [Google Scholar]
  27. Rainey F, Oren A. Taxonomy of Prokaryotes Amsterdam: Elsevier; 2011
    [Google Scholar]
  28. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  29. Collins MD. Analysis of isoprenoid quinones. In Gottschalk G. eds Methods in Microbiology New York: Academic Press; 1985 pp 329–366
    [Google Scholar]
  30. Kim D-U, Lee H, Lee S, Park S, Yoon J-H et al. Deinococcus multiflagellatus sp. nov., isolated from a car air-conditioning system. Antonie Van Leeuwenhoek 2018; 111:619–627 [View Article] [PubMed]
    [Google Scholar]
  31. Im W-T, Jung H-M, Ten LN, Kim MK, Bora N et al. Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:2348–2353 [View Article]
    [Google Scholar]
  32. Lee J-J, Lee Y-H, Park S-J, Lim S, Jeong S-W et al. Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea. J Microbiol 2016; 54:537–542 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005531
Loading
/content/journal/ijsem/10.1099/ijsem.0.005531
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error